I'm trying to access the groups and nodes associated with a message through entity reference fields. When I create the message I am able to set values to the field og_group_ref and field_node_ref with the entity metadata wrapper, but when I load a message with message_load, those values in the object are empty.

Is there another way to get the values from fields added to the bundle?

@amitabu: I'm using hook_node_insert(). I've worked around the issue by calling entity_load directly and setting $reset to TRUE. I had to do that with node_load too to access the summary of the node in a callback. After I bypass the cache everything is available.